GelFAP v2.0

GelFAP v2.0 provides gene functional annotation and analysis for Gastrodia elata by integrating chromosome-level genome assemblies and comprehensive transcriptome data to support gene function discovery and regulatory network analysis.

Key Features:

• Integration of chromosome-level genomes: Incorporates newly released chromosome-level genome assemblies for Gastrodia elata to enable analyses based on updated genomic coordinates.
• Comprehensive transcriptome resources: Includes extensive transcriptome datasets for assessing gene expression patterns and co-expression relationships in Gastrodia elata.
• Sequence alignment and annotation: Performs sequence alignment against NR, TAIR, Uniprot and Swissprot for functional assignment.
• GO and KEGG annotation: Predicts Gene Ontology and KEGG pathway annotations using InterProScan and GhostKOALA.
• Gene family prediction: Identifies transcription factors and protein kinases with iTAK and detects families using HMMER and InParanoid.
• Analytical and visualization tools: Supports BLAST, GSEA, heatmap generation, JBrowse genome visualization, motif analysis and sequence extraction for downstream analyses.
• Co-expression network construction: Provides co-expression network resources derived from integrated genomic and transcriptomic data.

Scientific Applications:

• Flavonoid biosynthesis regulation: Enables analysis of transcription factors such as MYB, HB and NAC involved in regulation of flavonoid biosynthesis in Gastrodia elata.
• Gene-specific functional studies: Facilitates characterization of specific genes including C4H and GAFP4 in Gastrodia elata.
• Molecular basis of medicinal traits: Supports investigation of genes and pathways underlying the medicinal properties of Gastrodia elata.

Methodology:

Computational methods explicitly include sequence alignment against NR, TAIR, Uniprot and Swissprot; GO and KEGG annotation with InterProScan and GhostKOALA; gene family prediction using iTAK, HMMER and InParanoid; analytical procedures including BLAST, GSEA, heatmap generation, JBrowse visualization, motif analysis and sequence extraction; and construction of a co-expression network by integrating chromosome-level genomes, transcriptome data and processed functional annotations.